Computational protocol: Identification of baboon microRNAs expressed in liver and lymphocytes

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Protocol publication

[…] Human pre-miRNA sequences were accessed from the University of California, Santa Cruz (UCSC) Genome Browser [,] utilizing the Table function for SNO/miRNAs []. The human pre-miRNA data in the Genome Browser are from the miRBase Sequence Database at the Wellcome Trust Sanger Institute [,]. Human pre-miRNA sequences were used to query the NCBI trace archives of the Papio hamadryas whole genome sequence using the BLASTN program http://blast.ncbi.nlm.nih.gov/Blast.cgi. BLAST alignment was optimized for highly similar sequences. Algorithm parameters included automatically adjusting for short input sequences, an expected threshold of 10, word size of 28, match/mismatch scores of 1-2, linear gap costs, and regional low complexity filtering. In addition, baboon to human sequence alignments were filtered based on baboon sequence quality scores greater than 50. Predicted baboon pre-miRNAs are shown in Additional File . [...] Human genomic DNA regions containing pre-miRNA clusters were identified by UCSC genome browser. Genomic DNA for each cluster was aligned with the draft assembly of the baboon genome sequence in the trace archive http://blast.ncbi.nlm.nih.gov/Blast.cgi using the BLAST alignment tool []. To validate baboon draft assembly alignment, the baboon genomic DNA region was aligned against the human genome using the BLAT alignment tool []. In addition, human genomic DNA was aligned with the rhesus genome using the BLAT alignment tool.Baboon genomic regions were aligned to regions of the other species by searching for homologous human miRNAs in the Baboon Test Genome Browser Gateway hosted by the UCSC http://genome-test.cse.ucsc.edu. BLAST was then used to search for baboon DNA sequences in the human genome for homologous region. Regional tracks of chimpanzee, rhesus, mouse and rat are also presented. […]

Pipeline specifications

Software tools BLASTN, BLAT
Databases UCSC Genome Browser
Applications WGS analysis, Genome data visualization
Organisms Papio ursinus, Homo sapiens
Diseases Cardiovascular Diseases, Dyslipidemias, Atherosclerosis